Render with alpha channel for transparency for After Effects?
Never render to video, always render to image sequence (PNG or EXR) and enable alpha output.

Rendering to video will mean you'll lose your entire render should your system crash or you have a power outage.

Sequences allow you to carry on rendering from where you were when the power went out or your system crashed.

Sequences in PNG allow for greater compatibility between programs, but the alpha channel will be unassociated alpha, so you won't be able to create objects that are luminous and transparent. EXR can do associated alpha correctly and you can keep your data linear. The EXR multilayer format will allow for the inclusion of compositing layers information, light, depth channels, diffuse, specular, transmission, etc.